Methods for identifying a nucleic acid in a sample are of great importance in clinical diagnosis, public health, veterinary health, biodefense, environmental science, and agriculture. For example, a particular pathogen in a sample can be identified and classified on the basis of its shape, growth characteristics, nutrient requirements, metabolic activity, presence of certain genes, expression of certain genes, etc. However, the process for separating and identifying pathogens is largely dominated by 19th century procedures of growing and isolating pure cultures. This is a slow and tedious process that works only for a small fraction of pathogens. Moreover, there are many pathogens that still cannot be isolated and identified in this manner.
There is a constant demand in the art for methods to identify nucleic acids in a sample. Certain aspects of this disclosure relate to such methods.